title: Aggressive assembly of pyrosequencing reads with mates.
abstract: BACKGROUND
  DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.
  
  
  RESULTS
  Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.
  
  
  BACKGROUND
  The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.
authors.affiliation: The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA. jmiller@jcvi.org
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.forename: Eli
authors.initials: E
authors.lastname: Venter
authors.forename: Brian P
authors.initials: BP
authors.lastname: Walenz
authors.forename: Anushka
authors.initials: A
authors.lastname: Brownley
authors.forename: Justin
authors.initials: J
authors.lastname: Johnson
authors.forename: Kelvin
authors.initials: K
authors.lastname: Li
authors.forename: Clark
authors.initials: C
authors.lastname: Mobarry
authors.forename: Granger
authors.initials: G
authors.lastname: Sutton
mesh_terms: D019295:Computational Biology / Q000379:methods; D016678:Genome; D023281:Genomics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software